Kondo, K. “Simulating the Impacts of Interregional Mobility Restriction on the Spatial Spread of COVID-19 in Japan,” Preprint at medRxiv. (2020)
https://doi.org/10.1101/2020.12.28.20248926

#from Github
if(!require(devtools)) install.packages("devtools")
#GRAPH
if(!require(ggplot2)) install.packages("ggplot2")
if(!require(ggrepel)) install.packages("ggrepel")
if(!require(scales)) install.packages("scales")
if(!require(patchwork)) devtools::install_github("thomasp85/patchwork")
if(!require(RColorBrewer)) install.packages("RColorBrewer")
#Dataframe
if(!require(tidyverse)) install.packages("tidyverse")
if(!require(readxl)) install.packages("readxl")
#Loop
if(!require(parallel)) install.packages("parallel")
if(!require(doParallel)) install.packages("doParallel")
if(!require(foreach)) install.packages("foreach")
#Shapefile
if(!require(sf)) install.packages("sf")
#Map Visualization
if(!require(tmap)) install.packages("tmap")

1 OD Matrix

This code chunk creates figures of OD matrix used in the manuscript. Open output/fig/paper directory.

#OD Matrix
source("r/spatial_seir_make_figure_odmatrix.R", echo = TRUE, prompt.echo = "")

2 Map Visualization

This code chunk creates maps used in the manuscript. Open output/fig/paper directory.

#Map Visualization
source("r/spatial_seir_make_figure_map.R", echo = TRUE, prompt.echo = "")

3 Simulation Results in Senario 4

3.1 Degree of NPIs

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3.2 Ratio of Daytime and Nighttime Force of Infection

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3.3 Number of Infectious Individuals

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4 Simulation Results in Senario 5

4.1 Degree of NPIs

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4.3 Number of Infectious Individuals

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